Conventional methods to identify leads for drug development involve primary screening of compound libraries for activity “hits,” followed by secondary screening to reduce the number of primary hits to a congeneric series of optimal leads for drug development.
The compound libraries, such as synthetic (e.g., combinatorial) and natural product (e.g., biological preparations and extracts) libraries, vary in size and complexity, ranging from hundreds, thousands, to millions or more of related or diverse compounds. The smaller libraries usually are well defined and each of the compounds frequently are contained in a separate storage or test vessel (e.g., dry or liquid form of the compound residing in a well of a multi-well storage or test plate with other members of the library). Larger libraries often are deconvolution and chemical analyses are typically performed in parallel to isolate and characterize the compound(s) responsible for the observed activity. Information gleaned from the initial screening and testing process also is used for subsequent rounds of analog synthesis (analog/focused libraries) and convergent screening and testing of particular analogs (i.e., iterative process). Computer-implemented theoretical or virtual compound libraries also provide a repository from which activity hits are selected for known or predicted structure-activity relationships.
Primary activity screening of compound libraries is based on selection of compounds that directly or indirectly interact with a specific biological receptor(s) (i.e., receptor-dependent activity screening). Isolated receptors and cells expressing single or combinations of receptors chosen to mimic a particular biological system or disease state generally provide the context of an assay for receptor-dependent activity screening. For high-throughput screening of larger libraries, automated systems utilizing multi-well arrays representing isolated receptors or cells that express them are the standard.
The driving force behind receptor-dependent activity screening as the primary approach for sifting through compound libraries is simple. Drugs (pharmacological/toxicological agent) elicit a pharmacological response through interaction with one or more biological receptors (drug/receptor-specific interaction). Thus, compounds that interact with a particular receptor or combination of receptors are presumed to be the most promising candidates for exhibiting some mutual activity in vivo and thus targets for secondary screening.
Compounds identified from a primary screen are then subjected to successively more focused and quantitative rounds of screening and validation to eliminate false positives and identify those exhibiting optimal biological activity against a target receptor(s) in an in vivo setting. This typically involves a combination of physiochemical and biological testing, including structural characterization and biological studies using cells, tissues and animals. Compounds with the most promising biological activity are selected as leads for drug development.
Drug development involves scale up and detailed toxicity, pharmacodynamic and pharmacokinetic studies that are performed to characterize pharmacological efficacy. These studies are conducted not only to gauge whether a test compound has activity in an in vivo setting, but also to examine bioavailability to assess possible route of administration, delivery formulations and the amount of a test compound necessary over time to produce a therapeutic effect with little or acceptable side effects. A variety of cell, tissue and animal model assays typically are employed for such studies. A handful of compounds (e.g., 5-10) that pass these tests are then tested in scaled up animal studies for further characterization. A lead drug compound with the most promising results in animal studies is then tested in humans in clinical trials.
Pharmacokinetic studies are conducted to characterize the time-dependent concentration of a test compound in the body, which collectively depends on absorption, distribution, metabolism and elimination (ADME) of the compound following administration. For instance, in order to reach the site of action, a lead drug compound that is administered to a subject must first be absorbed across epithelial barriers, usually by passive diffusion and/or active uptake, into the systemic circulation. In the case of intravascular administration, absorption is instantaneous and complete. However, all other routes of administration involve an absorption step with the potential that only a fraction of the administered compound may be absorbed into systemic circulation.
Systemic blood then delivers the compound to cells and tissues in the body, where the likely receptor/site of action resides, but various parallel processes compete for the compound. The compound may reversibly bind with proteins (albumin, al-acid glycoprotein) in plasma, or in some instances with tissue proteins. This is important since an unbound compound is typically the form taken up by cells and tissues. These processes determine distribution of the compound.
In a process referred to as excretion or elimination, organs such as the kidney, lung and liver are able to remove an unchanged lead drug compound from systemic circulation. Alternatively, the compound may be metabolized by enzymes frequently localized in all tissues, but mainly in the liver. Such metabolism produces metabolites that are chemically different from the administered compound and generally are more readily excreted from the body (reduced lipid solubility). Often the pharmacological/toxicological activity of a metabolite is reduced compared to that of the parent compound.
Thus while a lead or collection of lead drug compounds may continue to exhibit promising activity profiles early in the drug development process, most fail to make it as a drug product because of poor bioavailability discovered in animals, or worse poor bioavailability not discovered until human clinical trials (e.g., gancyclovir). This unacceptably high and expensive failure rate can be attributed in large part to the biased nature of activity-based screening to identify primary hits ultimately used as lead drug candidates. For instance, activity screening is pursued from the mindset that the greater and more specific the compound-receptor interaction/activity, the more potent a compound, and thus the smaller the dose required and consequent lower potential for toxic side-effects, as well as cheaper product produced and sold. However, a potent compound exhibiting poor bioavailability might require a higher dose than a less potent compound exhibiting superior bioavailability; this less potent compound also may exhibit reduced dose related toxicity. Therefore, the majority of activity levels do not result in drug products.
Receptor-dependent screening and testing also provides little to no information as to the probable route of administration for an activity hit. As an example, a test compound selected for activity may ultimately require intravenous administration, which is a less preferred route of administration. Here again a different less potent compound overlooked or discarded from an activity screen for lower potency may have been a good candidate for a preferred extravascular form of administration (e.g., oral). An oral form would be cheaper to administer even if administered at a higher dose to compensate for lower potency.
The dogmatic process of screening compound libraries first by receptor activity likewise reduces the value of the libraries themselves. Newly obtained or previously screened compounds having true therapeutic potential due to superior bioavailability properties are likely never to make it into the drug development pipeline if they fail to pass the primary activity screening process. Also valuable physical and chemical information from compounds otherwise possessing good bioavailability profiles that are discarded or overlooked for having less than some preferred activity level will be lost and unavailable for future development of structurally related activity leads or synthesis of new libraries.
Accordingly, a need exists for identifying compounds that exhibit desired pharmacokinetic properties before the drug development process, as well as guidance for future synthesis. The present invention provides an unprecedented and counterintuitive approach to address these and other needs.